From Somak Roy and colleagues: Next-Generation Sequencing Informatics

Somak Roy,William A. LaFramboise,Yuri E. Nikiforov,Marina N. Nikiforova,Mark J. Routbort,John Pfeifer,Rakesh Nagarajan,Alexis B. Carter,Liron Pantanowitz, (2016) Next-Generation Sequencing Informatics. Archives of Pathology & Laboratory Medicine In-Press.

Early Online Release

Next-Generation Sequencing Informatics

Challenges and Strategies for Implementation in a Clinical Environment

Somak Roy, MD; William A. LaFramboise, PhD; Yuri E. Nikiforov, MD, PhD; Marina N. Nikiforova, MD; Mark J. Routbort, MD, PhD; John Pfeifer, MD, PhD; Rakesh Nagarajan, MD, PhD; Alexis B. Carter, MD; Liron Pantanowitz, MD

Reprints: Somak Roy, MD, Department of Pathology, University of Pittsburgh Medical Center, 3477 Euler Way, Rm 7028, Clinical Laboratory Building (CLB), Pittsburgh, PA 15213 (email: roys@upmc.edu).

Context.—Next-generation sequencing (NGS) is revolutionizing the discipline of laboratory medicine, with a deep and direct impact on patient care. Although it empowers clinical laboratories with unprecedented genomic sequencing capability, NGS has brought along obvious and obtrusive informatics challenges. Bioinformatics and clinical informatics are separate disciplines with typically a small degree of overlap, but they have been brought together by the enthusiastic adoption of NGS in clinical laboratories. The result has been a collaborative environment for the development of novel informatics solutions. Sustaining NGS-based testing in a regulated clinical environment requires institutional support to build and maintain a practical, robust, scalable, secure, and cost-effective informatics infrastructure.

Objective.—To discuss the novel NGS informatics challenges facing pathology laboratories today and offer solutions and future developments to address these obstacles.

Data Sources.—The published literature pertaining to NGS informatics was reviewed. The coauthors, experts in the fields of molecular pathology, precision medicine, and pathology informatics, also contributed their experiences.

Conclusion.—The boundary between bioinformatics and clinical informatics has significantly blurred with the introduction of NGS into clinical molecular laboratories. Next-generation sequencing technology and the data derived from these tests, if managed well in the clinical laboratory, will redefine the practice of medicine. In order to sustain this progress, adoption of smart computing technology will be essential. Computational pathologists will be expected to play a major role in rendering diagnostic and theranostic services by leveraging Big Data and modern computing tools.